Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for MTHFD1
Basic gene info.Gene symbolMTHFD1
Gene namemethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase
SynonymsMTHFC|MTHFD
CytomapUCSC genome browser: 14q24
Genomic locationchr14 :64854758-64926725
Type of geneprotein-coding
RefGenesNM_005956.3,
Ensembl idENSG00000100714
Description5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate cyclohydrolase, 10-formyltetrahydrofolate synthetaseC-1-tetrahydrofolate synthase, cytoplasmicC1-THF synthasecytoplasmic C-1-tetrahydrofolate synthase
Modification date20141207
dbXrefs MIM : 172460
HGNC : HGNC
Ensembl : ENSG00000100714
HPRD : 01403
Vega : OTTHUMG00000141309
ProteinUniProt: P11586
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFD1
BioGPS: 4522
Gene Expression Atlas: ENSG00000100714
The Human Protein Atlas: ENSG00000100714
PathwayNCI Pathway Interaction Database: MTHFD1
KEGG: MTHFD1
REACTOME: MTHFD1
ConsensusPathDB
Pathway Commons: MTHFD1
MetabolismMetaCyc: MTHFD1
HUMANCyc: MTHFD1
RegulationEnsembl's Regulation: ENSG00000100714
miRBase: chr14 :64,854,758-64,926,725
TargetScan: NM_005956
cisRED: ENSG00000100714
ContextiHOP: MTHFD1
cancer metabolism search in PubMed: MTHFD1
UCL Cancer Institute: MTHFD1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTHFD1 in cancer cell metabolism1. Cheng TYD, Makar KW, Neuhouser ML, Miller JW, Song X, et al. (2015) Folate‐mediated one‐carbon metabolism genes and interactions with nutritional factors on colorectal cancer risk: Women's Health Initiative Observational Study. Cancer. go to article

Top
Phenotypic Information for MTHFD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MTHFD1
Familial Cancer Database: MTHFD1
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM 114500; phenotype.
172460; gene+phenotype.
601634; phenotype.
Orphanet 268377; Total spina bifida aperta.
268384; Thoracolumbosacral spina bifida aperta.
268388; Lumbosacral spina bifida aperta.
268392; Cervical spina bifida aperta.
268397; Cervicothoracic spina bifida aperta.
268740; Upper thoracic spina bifida aperta.
268748; Total spina bifida cystica.
268752; Thoracolumbosacral spina bifida cystica.
268758; Lumbosacral spina bifida cystica.
268762; Cervical spina bifida cystica.
268766; Cervicothoracic spina bifida cystica.
268770; Upper thoracic spina bifida cystica.
DiseaseKEGG Disease: MTHFD1
MedGen: MTHFD1 (Human Medical Genetics with Condition)
ClinVar: MTHFD1
PhenotypeMGI: MTHFD1 (International Mouse Phenotyping Consortium)
PhenomicDB: MTHFD1

Mutations for MTHFD1
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTHFD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG955100MTHFD111197146488689564887081LOC100505782193334173956558239565720
BG180332GLT25D11203191769250717692709MTHFD1196672146491283764913313
W27097MTHFD125122146491542064915518MTHFD1114432146491501564915329
BE707197MTHFD1572146490581264905879UVRAG67432117585285075853215
AW581578PIGC91241172410948172411063MTHFD1107304146492498564926633
BG992574PRRC2C154001171561993171562378MTHFD1392517146491512964915254

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1  1 2       1
GAIN (# sample)        1       1
LOSS (# sample)   1  1 1        
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=55)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr14:64908845-64908845p.R653Q3
chr14:64898312-64898312p.A458A2
chr14:64884707-64884707p.T194P2
chr14:64892501-64892501p.W303*2
chr14:64908139-64908139p.A618T2
chr14:64892515-64892515p.N308T2
chr14:64886575-64886575p.E220G2
chr14:64902374-64902374p.I528V2
chr14:64921543-64921543p.D890N2
chr14:64898264-64898264p.L442L2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample35 121 2 41 162 110429
# mutation35 121 2 41 162 111429
nonsynonymous SNV24 91 1 31 152 17326
synonymous SNV11 3  1 1   1   41 3
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

Top
check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr14:64908171p.E220G2
chr14:64886575p.S79C2
chr14:64898264p.E628D2
chr14:64879239p.L442L2
chr14:64882081p.E121Q1
chr14:64906967p.A448V1
chr14:64891605p.A643T1
chr14:64909106p.I833I1
chr14:64898303p.V124M1
chr14:64921540p.L455F1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for MTHFD1 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

Top
Gene Expression for MTHFD1

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AMD1,ANKS6,CDC20,CTPS1,EXO5,COLGALT1,HMGA1,
IFRD1,MPP6,MTHFD1L,NIP7,NUP93,PABPC4,PLEKHG1,
PPP1R14C,PSAT1,TBPL1,ULBP1,YARS,YBX1,ZFP69B
ADORA3,C1RL,CASP4,EXOG,FAM20A,FAM57A,IFI16,
LOC541471,LYN,MTHFD1L,MYD88,OSMR,RASSF2,SAMSN1,
SELPLG,SLCO2B1,SULF2,TMEM173,TPM4,TUBA1B,UBASH3B

CAD,CCDC86,CDCA5,CTPS1,EFTUD2,LMNB2,MCM4,
MTHFD1L,NCAPD3,NCL,NLE1,NOLC1,POLR1A,SLC7A5,
SSRP1,STC2,TCP1,TRAP1,XPO5,XPOT,YARS
CALR,CRELD2,DNAJC10,GARS,HM13,HSP90B1,HSPA5,
HYOU1,IARS,IPO4,LRP8,MANF,MARS,MCM6,
MTHFD1L,PDIA4,PKM,RUVBL1,SLC38A5,SRM,YARS
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for MTHFD1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P11586; -.
ChemistryChEMBL CHEMBL2541; -.
Organism-specific databasesPharmGKB PA31236; -.
Organism-specific databasesCTD 4522; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00116methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapproved; nutraceuticalTetrahydrofolic acid
DB00157methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapproved; nutraceuticalNADH
DB02358methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseexperimentalLY374571
DB03461methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseexperimental2'-Monophosphoadenosine 5'-Diphosphoribose
DB04322methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseexperimentalLY249543
DB00145methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapproved; nutraceuticalGlycine
DB00133methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapproved; nutraceuticalL-Serine
DB00158methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapproved; nutraceuticalFolic Acid
DB00563methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetaseapprovedMethotrexate


Top
Cross referenced IDs for MTHFD1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas